7-137020404-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_046103.1(LOC349160):n.341+12390T>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 151,582 control chromosomes in the GnomAD database, including 23,050 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.54 (23049 hom., cov: 31)
  • Exomes 𝑓: 1.0 (1 hom.)
• Consequence: LOC349160 NR_046103.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.391

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.622 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC349160	NR_046103.1	n.341+12390T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000586239.5	n.273+12390T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.537 AC: 81404 AN: 151462 Hom.: 23023 Cov.: 31

Gnomad AFR AF: 0.628

Gnomad AMI AF: 0.562

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.565

Gnomad EAS AF: 0.102

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.547

Gnomad OTH AF: 0.541

GnomAD4 exome AF: 1.00 AC: 2 AN: 2 Hom.: 1 AF XY: 1.00 AC XY: 2 AN XY: 2

GnomAD4 genome AF: 0.537 AC: 81465 AN: 151580 Hom.: 23049 Cov.: 31 AF XY: 0.532 AC XY: 39396 AN XY: 74040

Gnomad4 AFR AF: 0.629

Gnomad4 AMR AF: 0.409

Gnomad4 ASJ AF: 0.565

Gnomad4 EAS AF: 0.102

Gnomad4 SAS AF: 0.267

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.547

Gnomad4 OTH AF: 0.535

Alfa AF: 0.445 Hom.: 1772

Bravo AF: 0.527

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	1.6
Dann	Benign	0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1378650; hg19: chr7-136705151;